Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

Kawaji, Hideya, Lizio, Marina, Itoh, Masayoshi, Kanamori-Katayama, Mutsumi, Kaiho, Ai, Nishiyori-Sueki, Hiromi, Shin, Jay W., Kojima-Ishiyama, Miki, Kawano, Mitsuoki, Murata, Mitsuyoshi, Ninomiya-Fukuda, Noriko, Ishikawa-Kato, Sachi, Nagao-Sato, Sayaka, Noma, Shohei, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Carninci, Piero and The FANTOM Consortium (2014) Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing. Genome Research, 24 4: 708-718. doi:10.1101/gr.156232.113

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Author Kawaji, Hideya
Lizio, Marina
Itoh, Masayoshi
Kanamori-Katayama, Mutsumi
Kaiho, Ai
Nishiyori-Sueki, Hiromi
Shin, Jay W.
Kojima-Ishiyama, Miki
Kawano, Mitsuoki
Murata, Mitsuyoshi
Ninomiya-Fukuda, Noriko
Ishikawa-Kato, Sachi
Nagao-Sato, Sayaka
Noma, Shohei
Hayashizaki, Yoshihide
Forrest, Alistair R. R.
Carninci, Piero
The FANTOM Consortium
Title Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
Publication date 2014-04-01
Sub-type Article (original research)
DOI 10.1101/gr.156232.113
Open Access Status DOI
Volume 24
Issue 4
Start page 708
End page 718
Total pages 11
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
Formatted abstract
CAGE (cap analysis gene expression) and RNA-seq are two major technologies used to identify transcript abundances as well as structures. They measure expression by sequencing from either the 5′ end of capped molecules (CAGE) or tags randomly distributed along the length of a transcript (RNA-seq). Library protocols for clonally amplified (Illumina, SOLiD, 454 Life Sciences [Roche], Ion Torrent), second-generation sequencing platforms typically employ PCR preamplification prior to clonal amplification, while third-generation, single-molecule sequencers can sequence unamplified libraries. Although these transcriptome profiling platforms have been demonstrated to be individually reproducible, no systematic comparison has been carried out between them. Here we compare CAGE, using both second- and third-generation sequencers, and RNA-seq, using a second-generation sequencer based on a panel of RNA mixtures from two human cell lines to examine power in the discrimination of biological states, detection of differentially expressed genes, linearity of measurements, and quantification reproducibility. We found that the quantified levels of gene expression are largely comparable across platforms and conclude that CAGE and RNA-seq are complementary technologies that can be used to improve incomplete gene models. We also found systematic bias in the second- and third-generation platforms, which is likely due to steps such as linker ligation, cleavage by restriction enzymes, and PCR amplification. This study provides a perspective on the performance of these platforms, which will be a baseline in the design of further experiments to tackle complex transcriptomes uncovered in a wide range of cell types.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
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Citation counts: TR Web of Science Citation Count  Cited 31 times in Thomson Reuters Web of Science Article | Citations
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Created: Fri, 27 Jun 2014, 00:12:34 EST by Cathy Fouhy on behalf of Aust Institute for Bioengineering & Nanotechnology